Pathologist's past
by superwholockian7437
Summary: Molly Hooper has more secrets than one would anticipate. Sherlolly, BAMF!Molly, AU-ish. I'm terrible at summaries but don't let that stop you from giving it a go.
1. Chapter 1

**Hello again everyone. This idea popped into my head one day and I just could not get it out until I actually wrote it. There will be another chapter in addition to this one. This is un-beta'd so please excuse any mistakes there are. This story takes place a year or two after Moriarty comes back so all that's over with. I own nothing(sadly).**

**I hope you enjoy :)**

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He rolled his head back, allowing his eyes to adjust to the light. He tried to move his hands but they were bound behind him. He looked around and saw that he was in a warehouse of some sort.

He winced as an injury made itself known. He struggled against his ties, hoping to at least make it out of the chair he was in.

He shut his eyes, retracing his steps as to how he managed to get himself in this situation.

**Xoxoxoxo**

_He stormed out of St. Barts, ignoring the voice behind him. She was pleading for him to stay._

_"__Sherlock please! Come back inside so we can talk. At least give me that."_

_Pathetic._

_She expected him to stay in the place where he had just witnessed her wrapped up in another mans arms._

_He waved down a cab and hastily got in before she could even get to the street._

_"__221B please."_

_**Xoxoxoxo**_

'Molly,' his mind all but yelled at him.

Did she know where he was? Would he ever get to see her again, be the reason why her eyes lit up? _No, _she doesn't matter anymore.

Back to the issue at hand.

**Xoxoxoxo**

_The cab continued going the expected path until it zoomed right past Baker street._

"_You were supposed to stop back there." The idiots he was surrounded by…_

_The back of the cabbie's head shook a bit as he laughed._

"_Not the destination I had in mind, ."_

'_Great,' he thought sourly, 'Another psychopath.'_

_He was about to declare his displeasure when another thought stopped him._

'_A distraction.'_

_He was ready to play a game._

_**Xoxoxoxo**_

He let out a groan of frustration. Things weren't adding up, he was missing something. He tried again to deduce his surroundings. Nothing useful.

It appeared that his head was still fuzzy from the sedative he was injected with.

He was trying again to remember certain events from the day when a door swung open. In walked a man, surprisingly young. He was no taller than Sherlock. He had shaggy, brown hair and a lean build. He was being followed by three muscular men. All were armed with handguns.

"And the detective wakes up. Good morning, sleeping beauty," said the young man, assumingly the leader.

He spoke cheerfully with an American accent. Peculiar.

"_Consulting_ detective," he corrected.

The man let out a laugh, looking at the others as if to signal them to join in. They did.

"Don't be like that. I'd hate to kill you before she arrives."

_That_ caught him off guard.

"Who?"

He couldn't think of any woman that he could be used against. Well there was _her_, but she was couldn't be associated with this. No, it had to be someone else.

"You don't know? I have reasons to believe that the both of you have gotten rather..._cozy_," he sneered.

"I can assure you that I have no clue of who you are referring to," he stated, sounding bored.

Another chuckle.

"Still at a loss? She really didn't tell you _anything _about her past? Ooh," he sang cheerfully "she must not trust you enough."

Sherlock had long since ran out of patience by then..

"Look…" he trailed off in hopes of getting a name for the face.

"Mason," he provided.

"Look, _Mason_, you must have gotten the wrong man. I do not know of anyo-"

"So you are not associates with ' '?" he asked, saying her name somewhat..._mockingly_.

His jaw dropped and his eyes widened.

"I'll take that as a yes," Mason concluded.

Sherlock narrowed his eyes and clenched his jaw.

"Leave her out of this. Whatever you want to do to me, fine. Just leave her alone."

Mason laughed again.

"She's the whole reason you're here, you ass. If she hadn't meddled with my fathers business, you wouldn't be sitting in that chair."

This didn't make sense. What did Molly have to do with this?

The large doors opened up once again, this time with a greater force. Molly Hooper stormed in.

She wore jeans and a white t-shirt underneath an unfamiliar black leather jacket. Some strands of her hair had escaped the braid and now flicked around her face, which had several cuts on it, though they were minor.

"Mason, let him go," she spoke with an authority he'd never heard before.

Mason looked at her with disgust. However, Sherlock didn't miss the flicker of fear in his eyes.

"Ah Molly dear, you've arrived early," Mason called out..

"He had nothing to do with this. You should know by now how much I detest repeating myself," she stated sternly.

Apparently she wasn't in the mood for pleasantries.

The next words exchanged between the two were lost to Sherlock. He was still trying to wrap his head around the fact that Molly was here. However, that also meant that she has been keeping something from him.

"I'm not here to negotiate with you. Let him go."

Mason tutted,"You really should know better Molls. I'm not trying to make a negotiation. Neither of you are leaving here alive. Simple as that."

'_Molls?_' Sherlock thought to himself.

"I don't have time for this," she said under her breath.

She reached into her jacket and pulled out a knife. The men who were anxiously waiting behind Mason stepped forward and stood defensively.

Sherlock could've sworn his heart skipped a beat. The fight they had shared hours before was the farthest thing from his mind. Molly wasn't strong enough to take down these men alone. They were both practically a foot taller than her and two times wider.

One advanced towards her and threw a punch. She blocked it and grabbed his shoulders, bringing him down to her forcefully and kneeing him in the groin. He yelped and doubled over in pain. She kicked him in the jaw, sending him backwards. Before he could reach the ground, she grabbed his shirt and pulled him forward. She struck his nose with the palm of her hand and let go of his shirt front, finally using her right arm to elbow him, rendering him unconscious.

One of the other ones were approaching her from behind.

"Molly!" Sherlock yelled, his voice slightly hoarse.

She turned around just as the thug grabbed her left hand and dug his nails into the pad of flesh underneath her thumb. From the view Sherlock had, he could vaguely see her clenching her jaw as the man twisted her wrist at an odd angle. She wrapped her free hand around his neck and pulled him to her. Simultaneously, she thrusted her head back and then forward and delivered a headbutt . He released his grip on her and stumbled backwards, rubbing his forehead.

This had given the final man enough time to remember he had a gun. In fact, they all did. He pulled it out and walked up behind Molly, pressing the barrel of the gun to the back of her skull.

"Drop the knife," he shouted,"now!"

She smiled slightly and turned around, showing no fear to the gun currently placed between her eyes.

"Just to be clear, it needs to be out of my hand and touching the floor, correct?"

His eyes flashed with anger.

"Put it down!" he shouted, flecks of spit flying from his lips.

"If you say so," Molly said, shrugging her shoulders.

Her grip on the handle tightened and she dropped down, stabbing him in the foot.

He let out a howl of pain and released his weapon.

Molly heard footsteps falling behind her. They were close but nothing to worry about.

"This might sting a bit," she told the man who was currently yelling profanities and had tears spilling from his eyes. She ripped her blade from his foot and he screamed in agony. She then grabbed him by his shoulders and pushed him down thrusting her knee forward, colliding it with his nose and chin. He fell sideways, unconscious.

Sherlock watched from his spot in the chair in utter bewilderment. Was this really the woman he had worked with for years?

Behind him, Mason cut the ropes that were surrounding his waist. He grabbed Sherlock by the back of his shirt.

"Stand up," he demanded.

Molly spun around but not quite in time and received a nasty punch to her cheekbone. She let out a shriek and shifted backward. The offender grinned and delivered a slap. And another. And another. He decided to throw in a punch or two.

In a matter of movements, she was on the ground, shielding herself against his attacks.

"Molly, no!" Sherlock yelled. He struggled against Masons hold to no avail.

Her assailant looked at Sherlock with a satisfied expression. One moment the two were glaring at each other, the next, the thug had joined Molly on the ground. She climbed atop of him and punched him relentlessly.

Soon her arms grew weak and her hits were getting slower. She picked up the front of his shirt, lifting his head and neck off the ground. She pulled out a gun from behind her back (apparently she did have one concealed) and hit the man with the handle.

She stood up wearily and dragged her arm across her face, wiping away a portion of the blood that had collected there. She looked up to see that Mason had trained his gun against Sherlock's temple.

She limped over and lifted her left hand, the one that held the gun, and aimed it at Mason. Sherlock noticed something shiny flicker near her wrist. It was the bracelet he bought her a year ago for her birthday. It was rather simple, the only pendant a small, silver star.

"Give. Him. Back."

Sherlock could feel the gun shaking against his head.

'_Great. I'm being held at gunpoint by a man who's probably never even shot a gun._'

"Can't do that Molls, I'm sorry. You know what my old man used to say. Leave no witnesses to the crimes you commit."

There it was again. That insufferable nickname. It sounded..._childish._

"So, you're willing to bleed for this man?"he asked.

"Quite frankly, I'm willing to kill for him. Would you like me to demonstrate?"

She flipped off the safety switch.

"Don't make me do this Mason."

Mason applied more pressure to the trigger, preparing to shoot.

Molly looked Sherlock in the eyes. She pulled the trigger once, twice, without so much as flinching.

Mason's gun clattered to the floor with a clang, followed by the loud thud of his limp body hitting the ground.

Molly ran over to Sherlock and walked behind him, drawing her knife and cutting him loose. He rubbed his sore wrists. His eyes skimmed over the body of Mason. She had shot him in the throat and chest.

Molly walked back and stood in front of him, kind eyes searching his entire body for any injuries. She cupped both his cheeks and brought him down to her level for a clearer view.

"Could you turn your head a bit? Thanks"

Her fingers gently touched his scalp, searching for any harm they may have inflicted upon him.

"Oh baby, they got you good. Skin isn't broken but there sure will be a hell of a bump."

Her hands once again fluttered around, poking and prodding to see if anything had been broken.

He grabbed her arms so she would stop.

"Molly."

She looked up at him, her eyes back to their normal innocence.

"Your injuries are far more significant than my own. We should really get you to a hospital." He said, a small smile playing on his lips.

She stood on her tiptoes and brought her lips to his. She tasted like blood and sweat with an underlining of vanilla. His hold on her arms loosened and landed on her hips. She placed her arms around his neck, pulling him down closer to him. He felt her gasp and pull back, hands flying to her lip. It had a deep cut in it.

"Sorry. I shouldn't have kissed you with my face all beat up like this. It's just-I'm so happy you're okay. I don't know what I would have done if you'd gotten hurt because of me." She said quietly, letting go of her grip and returning herself to her own height and him his.

He opened his mouth to question her about the whole thing, what she had done, why she did it and why she kept it from him but she spoke before he could.

"We need to get out of here," she claimed, rushing over to Mason's body. He could have sworn he saw remorse in her eyes.

She picked up his gun and handed it to Sherlock.

"Sherlock, I need you to trust me. I'm sure you have questions-"

"Plenty,"he cut in.

Molly ignored him and continued.

"-And I have answers, I do. I just need you to trust me right now," she requested.

He was taken aback a little bit. After everything they had been through, didn't she know that he would always trust her. The image of her and the strange man in the morgue flashed through his mind but he quickly dismissed it.

'_She must have a good reason for that,_' he reasoned.

"Always."

She smiled in appreciation and grabbed his hand to lead him out of the building.

They ran till they were safely outside. Molly stood in front of the entrance and glanced around. She bit her lip tugged him down an alley. Tucked away in a corner was a black motorcycle. She walked a few steps ahead of him and tossed him a helmet. He caught it and stared at her, trying to form a question.

"Whe-where did you get this?"

"I, uh, borrowed it."

He almost smiled. Almost.

"From who?" he challenged.

She thought for a second before answering,"I stole it off the side of the road. All in the name of saving you. Now let's go, you're driving."

He put on his helmet and got on the bike. She climbed on after him and they set off.

**Xoxoxoxo**

Molly opened up her front door and walked in, leaving Sherlock to shut and lock it. She disappeared into her bathroom and re-emerged with a first aid kit. He grabbed the kit from her and motioned for her to sit down.

Sherlock took a seat in front of her and brushed the hair out of her face.

First, he put on the gloves provided and stood up to wet a washcloth. He placed it on her face and carefully rubbed, making sure to cause as little amount of pain as possible but still thoroughly remove the dried blood, dirt, and sweat. Next, he grabbed antiseptic wipes and cleaned her would winced whenever he touched her nose or left cheek. He'd mumble his apologies and moved on to a different area.

Her eyes remained open the whole time, watching each move he made. He took her hand in his and cleaned off her knuckles. He applied the bandages to the cuts that were serious enough to need one.

"And why didn't we go to the hospital?" he asked.

She lightly shook her head and sighed.

"They ask too many questions. Too big of a risk."

He only nodded in response.

Once he was finished,she stood up and walked into her kitchen. She returned with an ice pack and four paracetamoland walked by him and handed him two of the pills. She then proceeded to walk behind him.

"Keep it right here and it should help the swelling should go down," she said as she placed it at the back of his skull.

"Thank you."

She lightly kissed the top of his head and walked over to her chair. She swallowed her pills dry and Sherlock copied her. They sat in silence for a minute or two, neither one wanting to speak first.

"You sure you want to know everything?" she asked hesitantly.

"Positive."

She let out a huff of air and looked him seriously in the eyes.

"Shall we begin?"

**To Be Continued…**

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**So, yeah. I can't believe I'm about to be one of those people but leaving a comment really does help me write faster and just makes me really happy, so leave a comment if you desire to do so. Seriously, I do a little dance and can't stop smiling every time I get one.**

**Till next time, dear readers.**


	2. Chapter 2

**Here's the final installment of this two-shot. I hope it lives up to your guys standards. I'm not overly happy with it but decided it was better than nothing. Enjoy :)**

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They sat across from each other, Sherlock with an inpatient look upon his face and Molly a fluttering feeling in her chest. Not the type of fluttering you get before a kiss but the kind you get before an important speech.

"What would you like to know first? Where I learned to fight? How I'm connected to Mason? Oh, how about why I kept it all from you?" she asked.

"The man in the morgue. Who is he?"

The fact that this was his first question he asked made the corners of her lips twitch.

"I know as much about him as you do. He came into the morgue and started asking me questions. Before you question my lack of suspicion, we're getting a new intern at Barts and I thought maybe that he was that. We heard you walking down the hall and he got this really panicked look on his face. Then he grabbed me by the shoulders and started snogging me. By the time I pushed him off, you were gone ,"she said, cringing at the memory.

Sherlock kept his usual stoic expression on, but she could see his posture relax a considerable amount.

"What else?" she asked, feeling slightly nauseous. She was more than willing to tell him anything he wanted but now that it was actually happening, she couldn't help the nervous buzz in her stomach.

"Everything."

"Obviously,"she scoffed and then silently apologized,"I meant any part specifically?"

"Mason."

She looked around quickly and then licked her lips.

"And you promise to stay calm?" she asked.

"Promise," he confirmed.

"Alright then. My father and I moved to America when I was fourteen and-"

"Why did you move?" he interrupted.

"I was getting to that."

"Do it faster."

It fully hit Molly now that she was no longer just his girlfriend, but that she was a case in need of solving. She'd seen him before where she couldn't help but worry about the emotional state of his clients after they'd talked to him for more than ten minutes. She herself was no stranger herself to his coldness and expected no special treatment.

"My father was originally from America. He went on a trip to London for his job and met my mother at a local shop. The two fell in love almost immediately. He remained in London and resigned from his job. They married a year later and three after that I came along. When I was thirteen my mother, she, um-" she stopped and cleared her throat, trying to decide how to form her next sentence,"My mother was murdered on her way home from work. Or at least that's what the police told us. My father thought otherwise. One night a few months after her funeral my dad told me to pack up and that we were leaving London. I was heart broken but complied. The next week we were on a plane and on our way to Seattle, Washington."

"That doesn't explain anything,"Sherlock rudely pointed out.

"Well, if you would shut up and stop interrupting me, I could get a lot more said,"she snapped.

He put up his hands in surrender,"My apologies. By all means, continue."

"Thank you,"she may be a case to him, but there was no reason for her to take his verbal abuse,"Where was I? Oh, My father and I left London and moved to a place right outside of Seattle. Once we had gotten all settled in, I met our neighbors; a young man my age and his father."

"Mason and his father,"Sherlock muttered.

"Exactly. Over time, Mason and I became close and before I knew it, I had a best friend. Mason was always kind and humorous. His father, however, always was a bit...odd. Whenever my dad was near him, he was polite and cheery but I could see through his act. In his eyes there was a hatred that I hadn't understood at the time."

Sherlock opened his mouth to speak again but was silenced by her glare.

"When I was sixteen, my dad told me a secret, a big one at that. Apparently, before he had met my mother, he worked for some kind of secret service in the states. Gave it all up for my mum actually. Sadly, he left some loose ends and it came and bit him in the ass. The people who killed my mum, they weren't random muggers, they were members of a gang my father had dealt with and seemingly disposed of. But-"

"But he hadn't. There was still one remaining member. Mason's dad." Sherlock filled in, putting the pieces together.

She nodded and took a deep breath,"Some fathers taught their daughters how to ride a bike where as mine taught me things like how to dislocate a shoulder or how to take apart and be able to put it back together again. By the time I was eighteen I was the perfect little soldier. A year before I started college I worked jobs with him. Little missions like taking out a drug ring or breaking into offices and obtaining files."

"Why did you stop?"Sherlock asked.

She looked down and blinked away the tears that were already forming,"My father was told he had a brain tumor about two months after I had joined. It was inoperable, the doctor had given him two years at most. God, what I would give for him to have been right,"she took a deep, shuddering breath and continued,"He died five months later. I tried to continue doing work like usual but it was too painful. Everywhere I went, every job I worked, there were constant reminders of him."

"So you escaped."he said, almost to himself

Molly stood then and walked to the kitchen. He could hear the clanging of metal and the water being turned on.

"I have a feeling this conversation is going to be a long one so I'm making tea. Plus tea puts everyone in a good mood,"she called out.

She returned and offered him his cup and settled back down into her own seat. She began speaking as she sat down.

"Did I answer your question?"

"You talked to me about your father, where you learned to fight, your mother, and why you left. I wanted to know about Mason."

"I already told that we were friends when I was younger."

"Was your relationship only friendship?"

She looked at him skeptically,"Why does it matter?"

"Why won't you answer the question?"he retorted.

She mentally cursed at herself.

"Fine. No, it was not purely platonic. He was my boyfriend for about two years. I ended it when my father told me about Mason's father and everything he's done. End of story."

Sherlock knew he shouldn't feel jealous seeing as he was now the one who had her love but he still was uncomfortable at the thought.

"Molls. Why Molls?"he asked.

She clenched her jaw and looked at him,"My father called me Molls. It was his sick way of taunting me."

There was a silence between them as Sherlock looked at Molly and she stared back, her eyes saying a million different things. He was the first to speak.

"Why did Mason kidnap me?"

She placed her cup on the table and leaned forward.

"About four months ago a body was sent into the morgue. It was ruled off as a suicide but I just didn't believe it. When I did the autopsy, I discovered a strange mark under the man's ear. It was familiar in a deja vu sense, I just didn't know why. Later, the brother came in to identify the body and fill some things out. The brother, however, was Mason. Mason was a single child his whole life. When I hugged him-"

"You hugged him?"Sherlock asked incredulously.

Molly laughed slightly at Sherlock being so blatantly jealous.

"Yes. That is something you do when you greet old friends. Anyways, I looked under his ear when I hugged him and he had the same tattoo. That's when I realized why it looked so familiar. It's a gang symbol. Mason's father had one just like it. I asked Mason why he was in London and he said something about taking care of some business. I also asked him about his father and it turns out that his father passed away a few years back."

"Wasn't his father the leader of everything? Why did he need to lure you out?"asked Sherlock, who was still confused.

"Yes and I may have followed him after he left and disposed of four crates of high class drugs,"she admitted quietly.

His face twisted into one of equal anger and concern.

"You could've been killed, Molly! What were you thinking?"

She scoffed in disbelief.

"Pot meet kettle. You risk your life every other day like it's nothing. I can quite obviously take care of myself,"she argued.

He was quiet after that and just looked at her curiously. She felt guilty. She knew that he was concerned about her and wanted her to be safe but she thought that she had proven she was capable of protecting herself.

He then asked the question that he had been thinking about the whole time.

"Why did you keep it from me?"

"Honestly, it's a part of my past I'd love to forget. Maybe then I wouldn't feel so damn disgusted with myself for having to hide my past from everyone because the truth would make them fear me. I've thought about telling you, Sherlock, countless times. But thought of you hating me was too much to bear. It was a risk that I couldn't take."

She wiped away a tear that had rolled down her cheek and looked at Sherlock. He had closed his eyes and brought his hands in a prayer position to his face.

'_Leave it to him to go to his mind palace to figure out how to respond_' she thought somewhat admiringly.

For her, the silence was deafening. She stood up and walked to her bedroom, figuring that he'd be in his head for awhile. She stopped right before she entered.

"Sherlock,"she spoke, her back still to him,"you'd better listen. Whatever we have- this weird and nutty relationship- it's ours, and I intend to fight for it. I don't care how long it takes but losing you would hurt more than I can possibly imagine. It may not be easy but I can tell you now that it will sure as hell be worth it. Remember that."

She disappeared behind the door, leaving him by himself

Sherlock sat in the chair with his eyes open, staring at the spot she had just stood. It baffled him that she thought that he was ever going to leave her.

He then thought again of how she had been able to keep her secret from.

'_There's always something I miss_' he thought.

He closed his eyes once again and ventured back into his mind palace, going over every memory with Molly and seeing if he'd now be able to deduce her past.

Molly lied in bed, her aching body begging for sleep. She couldn't though. Her mind was all over the place. She tossed and turned, kicked off the blankets and put them back on again, even switched sides a couple times. She gave up after thirty minutes and lied stiffly. She replayed the days events and tried to decide a better outcome. She thought about what was to happen when Mason's body was discovered.

The door creaked open and all her thoughts vanished. Molly shut her eyes and pretended to sleep. She felt the mattress dip underneath his weight. She willed her heart to stop beating so frantically and for her breathing to steady.

He slid his arms around her waist and pulled her snugly to his body. He pressed a kiss to her neck and whispered in her ear,"I know you're awake, Molly. I need you to listen and listen closely. I am one of the most irritable and selfish man in all of London. I can be blunt and cruel, I've ignored you for days while working a case and have left at the drop of a hat. You on the other hand, are the picture of home. You're forgiving and loving, you bake when you're sad and watch crap telly with me. Now I don't know how I've managed to capture your love, but I don't for one second question it. No matter what happens, no matter the consequences, I promise to always be by your side. There is nothing on this planet that could ever convince me that you are not worth it, because you are. You, Molly Hooper, count more than you will ever know."

She turned and cupped his face before crashing her lips to his. Sherlock's grip on her tightened as he enthusiastically responded. It was insane and chaotic yet tender and absolutely perfect. They parted, breathing heavily and kept their foreheads touching.

"Toujours?"he asked delicately, his lips ghosting over hers.

She smiled softly and whispered,"Toujours,"before claiming his lips with hers once again.

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**Toujours means 'Always' in French(according to Google).**

**If you liked it don't be afraid to leave a comment. Much love and thank you to all those who followed, Favorited and left responses. Shout out to Sherlolly-shipper221B who has helped me and been encouraging me to post, you should totally check out her stories.**

**Again, thank you all!**


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